Variant report

Variant	rs4856739
Chromosome Location	chr3:160986710-160986711
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160980523..160999163-chr3:161073509..161094838,104	MCF-7	breast:
2	chr3:160818488..160819208-chr3:160986162..160986951,2	MCF-7	breast:
3	chr3:160937027..160941801-chr3:160984412..160987578,5	MCF-7	breast:
4	chr3:160980213..160981997-chr3:160984897..160987351,2	MCF-7	breast:
5	chr3:160985097..160988877-chr3:161008569..161012184,4	MCF-7	breast:
6	chr3:160977108..160997706-chr3:161077424..161093939,169	MCF-7	breast:
7	chr3:160936882..160947576-chr3:160982516..160994324,28	MCF-7	breast:
8	chr3:160984342..160995741-chr3:161044454..161065477,51	MCF-7	breast:
9	chr3:160784979..160786656-chr3:160985367..160987693,2	MCF-7	breast:
10	chr3:160979328..160995719-chr3:161119748..161144811,174	MCF-7	breast:
11	chr3:160974756..160978821-chr3:160984556..160987132,3	MCF-7	breast:
12	chr3:160949577..160952173-chr3:160986686..160988434,2	MCF-7	breast:
13	chr3:160982688..160996909-chr3:161122010..161144833,109	MCF-7	breast:
14	chr3:160820825..160823286-chr3:160983994..160987478,3	MCF-7	breast:
15	chr16:31189692..31192633-chr3:160984941..160987637,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000243838	Chromatin interaction
ENSG00000240567	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000089280	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10804790	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1154701	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12486253	0.88[EUR][1000 genomes]
rs12493960	0.88[AMR][1000 genomes]
rs12495310	0.90[EUR][1000 genomes]
rs13083229	0.88[EUR][1000 genomes]
rs1382427	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1382428	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1478565	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1478568	0.89[EUR][1000 genomes]
rs1599374	0.88[AMR][1000 genomes]
rs1599376	0.88[AMR][1000 genomes]
rs1599378	0.88[AMR][1000 genomes]
rs1600209	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1609688	0.88[AMR][1000 genomes]
rs163328	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs189270	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1993891	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2404340	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28515190	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs336541	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs336543	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs336548	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs336567	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336568	0.87[EUR][1000 genomes]
rs336569	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336570	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336577	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs336579	0.81[EUR][1000 genomes]
rs336580	0.87[EUR][1000 genomes]
rs336582	0.87[EUR][1000 genomes]
rs336583	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336585	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336586	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs336589	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336590	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336591	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs336593	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs339101	0.82[AMR][1000 genomes]
rs3849524	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4273380	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4290817	0.88[EUR][1000 genomes]
rs4350933	0.89[EUR][1000 genomes]
rs4370045	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4414866	0.91[AMR][1000 genomes]
rs4470535	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4493448	0.88[EUR][1000 genomes]
rs4518145	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4560315	0.90[EUR][1000 genomes]
rs456611	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs459515	0.85[EUR][1000 genomes]
rs459697	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4597724	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs460508	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs462514	0.85[EUR][1000 genomes]
rs464766	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4856714	0.89[EUR][1000 genomes]
rs4856738	0.90[EUR][1000 genomes]
rs4856767	0.89[EUR][1000 genomes]
rs4856768	0.89[EUR][1000 genomes]
rs55688744	0.86[EUR][1000 genomes]
rs6441370	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441371	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441373	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6762645	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6765269	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6765270	0.88[AMR][1000 genomes]
rs6768818	0.88[EUR][1000 genomes]
rs6774276	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775627	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6789388	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791213	0.85[EUR][1000 genomes]
rs6794601	0.87[EUR][1000 genomes]
rs6809256	0.86[EUR][1000 genomes]
rs7611367	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7613227	0.84[EUR][1000 genomes]
rs7613358	0.88[EUR][1000 genomes]
rs7615592	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7623206	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7627528	0.89[EUR][1000 genomes]
rs7629987	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7632797	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7633186	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7636941	0.87[EUR][1000 genomes]
rs7638668	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7647327	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7652267	0.87[EUR][1000 genomes]
rs7653233	0.89[EUR][1000 genomes]
rs7653361	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs899275	0.85[EUR][1000 genomes]
rs9290073	0.85[EUR][1000 genomes]
rs9290074	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs975323	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9790314	0.89[EUR][1000 genomes]
rs9809522	0.90[EUR][1000 genomes]
rs9815222	0.89[EUR][1000 genomes]
rs9821201	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9834659	0.90[EUR][1000 genomes]
rs9839527	0.89[EUR][1000 genomes]
rs9846756	0.99[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9850455	0.89[EUR][1000 genomes]
rs9870059	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9872514	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4856739	SPTSSB	cis	Heart Left Ventricle	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160939800-160995800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:160941000-160993400	Weak transcription	Pancreas	Pancrea
3	chr3:160956400-160993000	Weak transcription	Esophagus	oesophagus
4	chr3:160966200-160987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:160966200-160993200	Weak transcription	Right Ventricle	heart
6	chr3:160968800-160992200	Weak transcription	Brain Angular Gyrus	brain
7	chr3:160970400-160995600	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:160970800-160995600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:160971000-160987400	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:160971000-160989000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:160971000-160993800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:160971000-160995400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:160971000-160995400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:160971200-160988800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr3:160971200-160995200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:160971200-160996000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr3:160971800-160993000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr3:160972200-160996600	Weak transcription	Brain Substantia Nigra	brain
19	chr3:160972400-160993800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:160972800-160995400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr3:160973200-160993200	Weak transcription	Gastric	stomach
22	chr3:160973400-160989000	Weak transcription	Fetal Thymus	thymus
23	chr3:160974600-160990000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:160975400-160995800	Weak transcription	Fetal Intestine Large	intestine
25	chr3:160976400-160989400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:160976600-160989200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:160976600-160995400	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr3:160976800-160991800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:160979200-160999800	Weak transcription	Psoas Muscle	Psoas
30	chr3:160981000-160993600	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:160981200-160990600	Weak transcription	HSMMtube	muscle
32	chr3:160982200-160989200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:160982200-160993000	Weak transcription	Ovary	ovary
34	chr3:160982200-160993400	Weak transcription	Lung	lung
35	chr3:160982200-160993400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:160982200-160994000	Weak transcription	Fetal Brain Female	brain
37	chr3:160982200-160994200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:160982200-160994400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:160982200-160994600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:160982200-160995000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:160982200-160995400	Weak transcription	Aorta	Aorta
42	chr3:160982400-160988800	Weak transcription	Left Ventricle	heart
43	chr3:160982400-160992400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:160982400-160993200	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:160982400-160993200	Weak transcription	Fetal Stomach	stomach
46	chr3:160982400-160996600	Weak transcription	Adipose Nuclei	Adipose
47	chr3:160982600-160989400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:160983000-160991200	Weak transcription	Primary B cells from cord blood	blood
49	chr3:160983200-160988800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:160983400-160990200	Weak transcription	HepG2	liver

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